{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T06:08:52Z","timestamp":1789711732035,"version":"4.0.1"},"reference-count":81,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Agricultural practices, including organic amendments and microbial inoculants, strongly influence soil microbial communities, which play a crucial role in maintaining soil function and structure. To identify an effective strategy for improving soil microbiome diversity and crop production, we assessed and compared the soil microbial community in fields treated with cattle manure amendment (MA), microbial inoculant (MI), and a mixture of cattle manure and microbial inoculant (MM), while an untreated field served as the control. We then evaluated treatment effects on soybean production. Microbial diversity analyses showed that MM treatment was associated with increased bacterial diversity in bulk soil, whereas a pronounced enhancement of fungal diversity was observed in the rhizosphere. Community composition analyses indicated the elevation of relative abundances of Acidobacteriota and Chloroflexi in bulk soil upon either treatment. Notably, the Proteobacteria, including the rhizobial genus\n                    <jats:italic>Ensifer<\/jats:italic>\n                    , was significantly enriched in the rhizosphere upon MM treatment, while the relative abundance of Ascomycota was increased in both bulk and rhizospheric soil upon MA treatment. To co-relate with these soil microbiome features, the MM treatment was shown to have the most significant effect on the soybean growth promotion, including the notably higher aboveground and underground fresh weight, plant height, accompanied with markedly more root nodules, than either MI or MA treatment. Collectively, our results suggest that the combined application of organic and microbial amendments effectively reshapes the soil microbiome by enhancing microbial diversity and enriching nitrogen-fixing bacteria in the rhizosphere, thereby promoting the nitrogen-fixing potential and productivity of soybean.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1939259","type":"journal-article","created":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T05:36:50Z","timestamp":1789709810000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Combined application of organic and microbial amendments reshapes soil microbiome diversity and improves soybean growth performance"],"prefix":"10.3389","volume":"17","author":[{"given":"Xuanqi","family":"Zhang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University","place":["Yangling, Shaanxi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjie","family":"Dou","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University","place":["Yangling, Shaanxi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qinqin","family":"Cao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University","place":["Yangling, Shaanxi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Guo","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University","place":["Yangling, Shaanxi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yifan","family":"Yin","sequence":"additional","affiliation":[{"name":"Agricultural College, Inner Mongolia Minzu University","place":["Tongliao, Inner Mongolia, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiwei","family":"Zhu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University","place":["Yangling, Shaanxi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengke","family":"Zeng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University","place":["Yangling, Shaanxi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiale","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University","place":["Yangling, Shaanxi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dejun","family":"Han","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University","place":["Yangling, Shaanxi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyu","family":"Qiang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University","place":["Yangling, Shaanxi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,18]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"D791-D797","DOI":"10.1093\/nar\/gkad1039","article-title":"The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered","volume":"52","author":"Abarenkov","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"ycae122","DOI":"10.1093\/ismeco\/ycae122","article-title":"Biological and experimental factors that define the effectiveness of microbial inoculation on plant traits: a meta-analysis","volume":"4","author":"Azarbad","year":"2024","journal-title":"ISME Commun"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"471","DOI":"10.1007\/s13213-012-0491-y","article-title":"A standardized method for the sampling of rhizosphere and rhizoplan soil bacteria associated to a herbaceous root system","volume":"63","author":"Barillot","year":"2012","journal-title":"Ann. 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